Unfortunately, these new browser-related protocols are being designed and developed by W3C and IETF in rather unorganized manner, not completely technically driven, but reflecting battles between Apple, Google and Microsoft, all trying to standardize their own technologies. Similarly, different browsers choose to adopt only certain standards or parts of standards which makes developer life extremely hard.
I have implemented both Media Source Extensions and WebRTC, so I think I can answer your question:
Media Source Extensions is just a player inside the browser.
You create a MediaSource object
https://developer.mozilla.org/en-US/docs/Web/API/MediaSource
and assign it to your video element like this
video.src = URL.createObjectURL(mediaSource);
Then your javascript code can fetch media segments from somewhere (your server or webserver) and supply to SourceBuffer attached to MediaSource, for playback.
WebRTC is not just a player, it is also a capture, encoding and sending mechanism. So it is a player too, and you use it a little differently from Media Source Extensions. Here you create another object: MediaStream object
https://developer.mozilla.org/en-US/docs/Web/API/MediaStream
and assign it to your video element like this
video.srcObject = URL.createObjectURL(mediaStream);
Notice that in this case the mediaStream object is not created directly by yourself, but supplied to you by WebRTC APIs such as getUserMedia.
So, to summarize, in both cases you use video element to play, but with Media Source Extensions you have to supply media segments by yourself, while with WebRTC you use WebRTC API to supply media. And, once again, with WebRTC you can also capture user's webcam, encode it and send to another browser to play, enabling p2p video chat, for example.
Media Source Extensions browsers adoption: http://caniuse.com/#feat=mediasource
WebRTC browsers adoption: http://iswebrtcreadyyet.com/